Proteome Discoverer Phosphopeptides Workshop

Phosphopeptide analysis is a critical aspect of understanding cellular signaling and disease mechanisms, yet it comes with its own set of challenges. Phosphopeptides are often present in low abundance compared to their non-phosphorylated counterparts, requiring an enrichment step as part of the sample preparation protocol. Phosphopeptides can be difficult to ionize and fragment efficiently in mass spectrometry, and specific instrument method settings should be employed to address that. Data analysis and interpretation is complicated as well, due to the presence of multiple phosphorylation sites on a single peptide and the potential for different phosphorylation states (e.g., mono-, di-, or tri-phosphorylation).

Addressing these challenges involves optimizing sample preparation protocols, using advanced mass spectrometry techniques, and employing robust bioinformatics tools to ensure accurate and comprehensive phosphopeptide analysis. This workshop will provide you with valuable insights and practical solutions to overcome these hurdles, enhancing your research capabilities.

What You Will Learn:

• Strategies for enriching low-abundance phosphopeptides
• Techniques to minimize phosphate group loss during sample preparation
• Advanced mass spectrometry methods for efficient phosphopeptide detection
• Best practices for data interpretation and bioinformatics analysis
• Case studies with hands-on data processing examples

The workshop is aimed at both novice and intermediate users. We planned time at the end of the workshop to answer our questions.

14:00 BST / 15:00 CEST – Welcome and start of the workshop

14:05 BST / 15:05 CEST – Sample preparation (Leigh Foster)

• Overview of workflows and products
• Cleanup considerations
• Enrichment methods
• Special applications

14:55 BST / 15:55 CEST – LC-MS acquisition methods (Jenny Ho)

• Fragmentation techniques for phosphopeptide characterization
• Relative quantitation (TM, DIA)

15:45 BST / 16:45 CEST – Data processing (Michaela Scigalova)

• Decision tree based on acquisition parameters
• Workflows and parameter settings
• Visualization of results
• Relative quantitation of TMT-labeled phosphopeptides

16:30 BST / 17:30 CEST – Close

You are unable to attend the webinar broadcast on September 17? Please register anyway to automatically receive the link to the recording.

Presenter: Leigh Foster (Scientist, Mass Spectrometry and Immunoassay Systems, Thermo Fisher Scientific)

Leigh Foster is a Scientist at Thermo Fisher Scientific. Her experience is in protein biology and she works in mass spectrometry reagent product development group based in Rockford, Illinois.

Presenter: Jenny Ho (Sr. Lab Application Scientist, LCMS Proteomics, Thermo Fisher Scientific)

Jenny Ho is a senior proteomics applications specialist at Thermo Fisher Scientific based in the Life Science Mass Spectrometry demonstration facility, in the UK.

Presenter: Michaela Scigelova (Product Support, Thermo Fisher Scientific)

Michaela provides customer support to Thermo Scientific Proteome Discoverer software users.